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9uab

Crystal structure of the OkaE-M64A mutant with coblat(II)

Method: X-RAY DIFFRACTION D_max: 116.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9uab
deposition_date	2025-03-31
title	Crystal structure of the OkaE-M64A mutant with coblat(II)
keywords	dioxygenase, non-heme, iron dependent, oxidoreductase; OXIDOREDUCTASE
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	34.84 Å
rg_electron	34.14 Å
i0	289322000.00
molecular_weight	132540.0 kDa
excluded_volume	164080 Å³
envelope_volume	206770 Å³
shell_volume	49758 Å³
envelope_diameter	126.7 Å
shell_rg	41.29 Å
envelope_rg	33.90 Å
shape_rg	34.15 Å
total_rg	34.62 Å
total_atoms	9284
n_residues	1173
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	116.8 Å
rg_real	34.81 Å
rg_real_error	0.87 Å
i0_real	2.8930e+08
i0_real_error	4.8740e+06
rg_reciprocal	34.83 Å
i0_reciprocal	289300000.0000
total_estimate	0.8847
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	38.9 Å
skewness	0.314
kurtosis	-0.343
angular_range	— – 0.2250 Å⁻¹
current_alpha	0.0000
highest_alpha	140300000.0000
n_real_points	46
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.859; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.924

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Iron/alpha-ketoglutarate-dependent dioxygenase okaE
formula_weight	35439.2 kDa
ec_number	1.14.-.-
mutation	M64A
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	9766

MGDRGPEFTLTENVMKPQIQRFTRDHDPKVLWQVVEEDGAVIIEGFLPHEVIQKFDCELDVRSKATKGGEANQEFYQMPVPTTTKWMNDLTATCPTFRHEILNNDILHSLCNVAFEPHGDYWLLNGMAMEMMPGNPTQQIHNDHGTHPILQYLRPDAPAPVFSIITAVTEFTESNGATRVILGSHRWPQGQKAKDDQAVRAALQPGDALVMHRSTKHGGAAHDADNQDHRRLLLTCMGTCQLAPYETNVTVPRPIVESMTPLAQKMIGWRSTRPVISNVTGLNTVRMKHLENQIELKSNVPLNVGGCWSHPQFEK

Source

organism	Penicillium simplicissimum
ncbi_taxonomy_id	69488
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	COBALT (II) ION
formula_weight	58.9 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	15

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	482

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6. Citations (1)

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length_a	76.352 Å
length_b	108.026 Å
length_c	134.515 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	P 21 21 21
int_tables_number	19
crystal_system	orthorhombic

resolution	2.550 Å
resolution_low	45.720 Å
r_factor	0.1909
r_work	0.1883
r_free	0.2395

fit	/app/data/saxs_computation/ua/9uab/9uab.fit
pddf	/app/data/pr_computation/ua/9uab/9uab.pr.out
profile	/app/data/saxs_computation/ua/9uab/9uab.dat

Crystal structure of the OkaE-M64A mutant with coblat(II)

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction